Python: module rosetta.protocols.anchored

rosetta.protocols.anchored_design

index
(built-in)

Bindings for protocols::anchored_design namespace

Classes



builtins.object

Anchor
AnchorMoversData

rosetta.protocols.moves.Mover(builtins.object)

AnchoredDesignMover
AnchoredPerturbMover
AnchoredRefineMover

class Anchor(builtins.object)

    Anchor class provides for the "anchor" part of a scaffold in anchored interface design Anchor class implements the code to read in an anchor file, stores the definition of the anchor, and provides access methods for setting move maps.  It reads in PDB-keyed information, but converts it to pose resid information and internally stores only the latter.

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.anchored_design.Anchor) -> NoneType 2. __init__(self : rosetta.protocols.anchored_design.Anchor, start : int, end : int) -> NoneType 3. __init__(self : rosetta.protocols.anchored_design.Anchor, pose : rosetta.core.pose.Pose, filename : str) -> NoneType 4. __init__(self : rosetta.protocols.anchored_design.Anchor, pose : rosetta.core.pose.Pose) -> NoneType 5. __init__(self : rosetta.protocols.anchored_design.Anchor, rhs : rosetta.protocols.anchored_design.Anchor) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.anchored_design.Anchor, rhs : rosetta.protocols.anchored_design.Anchor) -> rosetta.protocols.anchored_design.Anchor assignment operator

end(...) from builtins.PyCapsule
end(rosetta.protocols.anchored_design.Anchor) -> int returns end of anchor (as pose resid)

get_filename(...) from builtins.PyCapsule
get_filename(rosetta.protocols.anchored_design.Anchor) -> str getter for filename for anchorfile

read_anchorfile(...) from builtins.PyCapsule
read_anchorfile(*args, **kwargs) Overloaded function. 1. read_anchorfile(self : rosetta.protocols.anchored_design.Anchor, pose : rosetta.core.pose.Pose, filename : str) -> NoneType method to read an anchor file. Pose is necessary to reference against 2. read_anchorfile(self : rosetta.protocols.anchored_design.Anchor, pose : rosetta.core.pose.Pose) -> NoneType method to read an anchor file. Pose is necessary to reference against.  Checks internal data for filename.

read_options(...) from builtins.PyCapsule
read_options(rosetta.protocols.anchored_design.Anchor) -> NoneType read option system into internal data

set_filename(...) from builtins.PyCapsule
set_filename(self : rosetta.protocols.anchored_design.Anchor, filename : str) -> NoneType setter for filename for anchorfile

start(...) from builtins.PyCapsule
start(rosetta.protocols.anchored_design.Anchor) -> int returns start of anchor (as pose resid)

class AnchorMoversData(builtins.object)

    This data class wraps all the data needed for the AnchoredDesign movers. This data class keeps the anchor, mobile loops, and movemaps associated with the loops all together. It generates its own movemaps.

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(rosetta.protocols.anchored_design.AnchorMoversData) -> NoneType 2. __init__(rosetta.protocols.anchored_design.AnchorMoversData, rosetta.protocols.anchored_design.Anchor, rosetta.protocols.loops.Loops) -> NoneType doc 3. __init__(self : rosetta.protocols.anchored_design.AnchorMoversData, anchor : rosetta.protocols.anchored_design.Anchor, loops : rosetta.protocols.loops.Loops, options : bool) -> NoneType 4. __init__(self : rosetta.protocols.anchored_design.AnchorMoversData, pose : rosetta.core.pose.Pose) -> NoneType 5. __init__(self : rosetta.protocols.anchored_design.AnchorMoversData, rhs : rosetta.protocols.anchored_design.AnchorMoversData) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

anchor_end(...) from builtins.PyCapsule
anchor_end(rosetta.protocols.anchored_design.AnchorMoversData) -> int access for anchor end

anchor_noise_constraints_setup(...) from builtins.PyCapsule
anchor_noise_constraints_setup(self : rosetta.protocols.anchored_design.AnchorMoversData, pose : rosetta.core.pose.Pose) -> NoneType set up constraints for anchor_noise_constraints_mode

anchor_start(...) from builtins.PyCapsule
anchor_start(rosetta.protocols.anchored_design.AnchorMoversData) -> int //////////////////////////anchor functions////////////////////////////////////////////// access for anchor start

anchored_loop(...) from builtins.PyCapsule
anchored_loop(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.protocols.loops.Loop //////////////loops and movemap functions////////////////////////////////////////////// access anchored loop

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.anchored_design.AnchorMoversData, rhs : rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.protocols.anchored_design.AnchorMoversData assignment operator

autogenerate_constseq_frags(...) from builtins.PyCapsule
autogenerate_constseq_frags(self : rosetta.protocols.anchored_design.AnchorMoversData, seq : str) -> rosetta.core.fragment.FragSet brew its own sequence-specific frags

autogenerate_design_frags(...) from builtins.PyCapsule
autogenerate_design_frags(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.core.fragment.FragSet brew its own design frags (LLLLL secondary structure)

autogenerate_frags(...) from builtins.PyCapsule
autogenerate_frags(self : rosetta.protocols.anchored_design.AnchorMoversData, pose : rosetta.core.pose.Pose) -> NoneType figure out what type of fragments to use, and use them; pose needed to make packertask to detect if design is occuring

clone(...) from builtins.PyCapsule
clone(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.protocols.anchored_design.AnchorMoversData

get_VDW_weight(...) from builtins.PyCapsule
get_VDW_weight(rosetta.protocols.anchored_design.AnchorMoversData) -> float VDW weight in centroid scorefunction

get_akash_dyepos(...) from builtins.PyCapsule
get_akash_dyepos(rosetta.protocols.anchored_design.AnchorMoversData) -> int dye position used in dye modeling publication

get_allow_anchor_repack(...) from builtins.PyCapsule
get_allow_anchor_repack(rosetta.protocols.anchored_design.AnchorMoversData) -> bool allow anchor to repack

get_anchor_noise_constraints_mode(...) from builtins.PyCapsule
get_anchor_noise_constraints_mode(rosetta.protocols.anchored_design.AnchorMoversData) -> bool special anchor_noise_constraints_mode

get_anchor_via_constraints(...) from builtins.PyCapsule
get_anchor_via_constraints(rosetta.protocols.anchored_design.AnchorMoversData) -> bool used to test anchoring via constraints

get_centroid_scorefunction(...) from builtins.PyCapsule
get_centroid_scorefunction(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.core.scoring.ScoreFunction access centroid scorefunction

get_centroid_scorefunction_min(...) from builtins.PyCapsule
get_centroid_scorefunction_min(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.core.scoring.ScoreFunction access centroid scorefunction for minimization

get_chainbreak_weight(...) from builtins.PyCapsule
get_chainbreak_weight(rosetta.protocols.anchored_design.AnchorMoversData) -> float chainbreak weight in fullatom scorefunction

get_frag3(...) from builtins.PyCapsule
get_frag3(rosetta.protocols.anchored_design.AnchorMoversData) -> str copy of cmdline option frag3

get_frags(...) from builtins.PyCapsule
get_frags(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.core.fragment.FragSet /////////////////////scfxn, packertask, fragments accessors////////////////////////////// access fragments object

get_fullatom_scorefunction(...) from builtins.PyCapsule
get_fullatom_scorefunction(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.core.scoring.ScoreFunction access fullatom scorefunction

get_late_factory(...) from builtins.PyCapsule
get_late_factory(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.core.pack.task.TaskFactory access packertask factory

get_loop_file(...) from builtins.PyCapsule
get_loop_file(rosetta.protocols.anchored_design.AnchorMoversData) -> str copy of cmdline option loop_file

get_no_frags(...) from builtins.PyCapsule
get_no_frags(rosetta.protocols.anchored_design.AnchorMoversData) -> bool do not use fragments?

get_resfile_1(...) from builtins.PyCapsule
get_resfile_1(rosetta.protocols.anchored_design.AnchorMoversData) -> str resfile for design

get_resfile_2(...) from builtins.PyCapsule
get_resfile_2(rosetta.protocols.anchored_design.AnchorMoversData) -> str later-stage resfile if desired

get_super_secret_fixed_interface_mode(...) from builtins.PyCapsule
get_super_secret_fixed_interface_mode(rosetta.protocols.anchored_design.AnchorMoversData) -> bool special super_secret_fixed_interface_mode

get_task(...) from builtins.PyCapsule
get_task(self : rosetta.protocols.anchored_design.AnchorMoversData, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.PackerTask return packertask from factory

get_task_factory(...) from builtins.PyCapsule
get_task_factory(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.core.pack.task.TaskFactory access packertask factory

get_unbound_mode(...) from builtins.PyCapsule
get_unbound_mode(rosetta.protocols.anchored_design.AnchorMoversData) -> bool used for unbound mode

interface_calc(...) from builtins.PyCapsule
interface_calc(rosetta.protocols.anchored_design.AnchorMoversData) -> str get string name for interface_calc_

loop(...) from builtins.PyCapsule
loop(self : rosetta.protocols.anchored_design.AnchorMoversData, i : int) -> rosetta.protocols.loops.Loop accessor for a loop

loops(...) from builtins.PyCapsule
loops(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.protocols.loops.Loops accessor for loops object

movemap_cen(...) from builtins.PyCapsule
movemap_cen(self : rosetta.protocols.anchored_design.AnchorMoversData, i : int) -> rosetta.core.kinematics.MoveMap accessor for omega-variable movemap (most movers); centroid phase (no anchor movement)

movemap_cen_all(...) from builtins.PyCapsule
movemap_cen_all(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.core.kinematics.MoveMap access for movemap that covers all loops; centroid

movemap_cen_omegafixed(...) from builtins.PyCapsule
movemap_cen_omegafixed(self : rosetta.protocols.anchored_design.AnchorMoversData, i : int) -> rosetta.core.kinematics.MoveMap accessor for omega-fixed movemap (appropriate for CCD movers); centroid phase

movemap_fa(...) from builtins.PyCapsule
movemap_fa(self : rosetta.protocols.anchored_design.AnchorMoversData, i : int) -> rosetta.core.kinematics.MoveMap accessor for omega-variable movemap (most movers); fullatom phase (may allow anchor movement w/constraints)

movemap_fa_all(...) from builtins.PyCapsule
movemap_fa_all(rosetta.protocols.anchored_design.AnchorMoversData) -> rosetta.core.kinematics.MoveMap access for movemap that covers all loops; fullatom

movemap_fa_omegafixed(...) from builtins.PyCapsule
movemap_fa_omegafixed(self : rosetta.protocols.anchored_design.AnchorMoversData, i : int) -> rosetta.core.kinematics.MoveMap accessor for omega-fixed movemap (appropriate for CCD movers); fullatom phase (may allow anchor movement w/constraints)

neighborhood_calc(...) from builtins.PyCapsule
neighborhood_calc(rosetta.protocols.anchored_design.AnchorMoversData) -> str get string name for neighborhood_calc_

num_loops(...) from builtins.PyCapsule
num_loops(rosetta.protocols.anchored_design.AnchorMoversData) -> int number of loops/mms

pick_new_cutpoints(...) from builtins.PyCapsule
pick_new_cutpoints(self : rosetta.protocols.anchored_design.AnchorMoversData, reset_always : bool) -> NoneType randomly reset loop cutpoints.  Useful only when starting structure is well-closed.  Best for MPI-style runs

read_options(...) from builtins.PyCapsule
read_options(rosetta.protocols.anchored_design.AnchorMoversData) -> NoneType read options from the option system

set_VDW_weight(...) from builtins.PyCapsule
set_VDW_weight(self : rosetta.protocols.anchored_design.AnchorMoversData, VDW_weight : float) -> NoneType VDW weight in centroid scorefunction

set_akash_dyepos(...) from builtins.PyCapsule
set_akash_dyepos(self : rosetta.protocols.anchored_design.AnchorMoversData, akash_dyepos : int) -> NoneType /////////////option system replacement///////////////////////////// dye position used in dye modeling publication

set_allow_anchor_repack(...) from builtins.PyCapsule
set_allow_anchor_repack(self : rosetta.protocols.anchored_design.AnchorMoversData, allow_anchor_repack : bool) -> NoneType allow anchor to repack

set_anchor_noise_constraints_mode(...) from builtins.PyCapsule
set_anchor_noise_constraints_mode(self : rosetta.protocols.anchored_design.AnchorMoversData, anchor_noise_constraints_mode : bool) -> NoneType special anchor_noise_constraints_mode

set_anchor_via_constraints(...) from builtins.PyCapsule
set_anchor_via_constraints(self : rosetta.protocols.anchored_design.AnchorMoversData, anchor_via_constraints : bool) -> NoneType used to test anchoring via constraints

set_centroid_scorefunction(...) from builtins.PyCapsule
set_centroid_scorefunction(self : rosetta.protocols.anchored_design.AnchorMoversData,  : rosetta.core.scoring.ScoreFunction) -> NoneType set centroid scorefunction

set_chainbreak_weight(...) from builtins.PyCapsule
set_chainbreak_weight(self : rosetta.protocols.anchored_design.AnchorMoversData, chainbreak_weight : float) -> NoneType chainbreak weight in fullatom scorefunction

set_frag3(...) from builtins.PyCapsule
set_frag3(self : rosetta.protocols.anchored_design.AnchorMoversData, frag3 : str) -> NoneType copy of cmdline option frag3

set_frags(...) from builtins.PyCapsule
set_frags(self : rosetta.protocols.anchored_design.AnchorMoversData,  : rosetta.core.fragment.FragSet) -> NoneType ////////////////set functions///////////////////////////////////////////////////////// set fragments object

set_fullatom_scorefunction(...) from builtins.PyCapsule
set_fullatom_scorefunction(self : rosetta.protocols.anchored_design.AnchorMoversData,  : rosetta.core.scoring.ScoreFunction) -> NoneType set fullatom scorefunction

set_loops_and_anchor(...) from builtins.PyCapsule
set_loops_and_anchor(self : rosetta.protocols.anchored_design.AnchorMoversData, anchor : rosetta.protocols.anchored_design.Anchor, loops : rosetta.protocols.loops.Loops) -> NoneType set up kinematics' loops and anchors

set_no_frags(...) from builtins.PyCapsule
set_no_frags(self : rosetta.protocols.anchored_design.AnchorMoversData, no_frags : bool) -> NoneType do not use fragments?

set_resfile_1(...) from builtins.PyCapsule
set_resfile_1(self : rosetta.protocols.anchored_design.AnchorMoversData, resfile_1 : str) -> NoneType resfile for design

set_resfile_2(...) from builtins.PyCapsule
set_resfile_2(self : rosetta.protocols.anchored_design.AnchorMoversData, resfile_2 : str) -> NoneType later-stage resfile if desired

set_super_secret_fixed_interface_mode(...) from builtins.PyCapsule
set_super_secret_fixed_interface_mode(self : rosetta.protocols.anchored_design.AnchorMoversData, super_secret_fixed_interface_mode : bool) -> NoneType special super_secret_fixed_interface_mode

set_task_factory(...) from builtins.PyCapsule
set_task_factory(self : rosetta.protocols.anchored_design.AnchorMoversData,  : rosetta.core.pack.task.TaskFactory) -> NoneType set packertask factory

set_unbound_mode(...) from builtins.PyCapsule
set_unbound_mode(self : rosetta.protocols.anchored_design.AnchorMoversData, unbound_mode : bool) -> NoneType used for unbound mode

class AnchoredDesignMover(rosetta.protocols.moves.Mover)


Method resolution order:

AnchoredDesignMover

rosetta.protocols.moves.Mover

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(self : handle, interface_in : protocols::anchored_design::AnchorMoversData) -> NoneType 2. __init__(handle) -> NoneType 3. __init__(handle, rosetta.protocols.anchored_design.AnchoredDesignMover) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

apply(...) from builtins.PyCapsule
apply(self : rosetta.protocols.anchored_design.AnchoredDesignMover, pose : rosetta.core.pose.Pose) -> NoneType

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.anchored_design.AnchoredDesignMover, rhs : rosetta.protocols.anchored_design.AnchoredDesignMover) -> rosetta.protocols.anchored_design.AnchoredDesignMover assignment operator

calculate_rmsd(...) from builtins.PyCapsule
calculate_rmsd(self : rosetta.protocols.anchored_design.AnchoredDesignMover, pose : rosetta.core.pose.Pose, start_pose : rosetta.core.pose.Pose) -> NoneType calculate RMSD if desired; protected internally

clone(...) from builtins.PyCapsule
clone(rosetta.protocols.anchored_design.AnchoredDesignMover) -> rosetta.protocols.moves.Mover

delete_interface_native_sidechains(...) from builtins.PyCapsule
delete_interface_native_sidechains(self : rosetta.protocols.anchored_design.AnchoredDesignMover, pose : rosetta.core.pose.Pose) -> NoneType This function repacks the interface with use_input_sc forcibly off for benchmarking purposes.

filter(...) from builtins.PyCapsule
filter(self : rosetta.protocols.anchored_design.AnchoredDesignMover, pose : rosetta.core.pose.Pose) -> NoneType runs varous filtering checks on the finished pose; sets MoverStatus for failure as needed

forget_initial_loops(...) from builtins.PyCapsule
forget_initial_loops(self : rosetta.protocols.anchored_design.AnchoredDesignMover, pose : rosetta.core.pose.Pose) -> NoneType implements the "extended" field of the loop file specification - sets extended phi/psi as needed

fresh_instance(...) from builtins.PyCapsule
fresh_instance(rosetta.protocols.anchored_design.AnchoredDesignMover) -> rosetta.protocols.moves.Mover

get_RMSD_only_this(...) from builtins.PyCapsule
get_RMSD_only_this(rosetta.protocols.anchored_design.AnchoredDesignMover) -> str run only RMSD calculations against this input, don't do actual AnchoredDesign

get_autoinitialize(...) from builtins.PyCapsule
get_autoinitialize(rosetta.protocols.anchored_design.AnchoredDesignMover) -> bool whether to automatically initialize from the options system; defaults to true

get_delete_interface_native_sidechains(...) from builtins.PyCapsule
get_delete_interface_native_sidechains(rosetta.protocols.anchored_design.AnchoredDesignMover) -> bool delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode

get_filter_SASA(...) from builtins.PyCapsule
get_filter_SASA(rosetta.protocols.anchored_design.AnchoredDesignMover) -> float filter based on complex SASA

get_filter_omega(...) from builtins.PyCapsule
get_filter_omega(rosetta.protocols.anchored_design.AnchoredDesignMover) -> bool filter based on omega angles in the loops - filter out cis omegas

get_filter_score(...) from builtins.PyCapsule
get_filter_score(rosetta.protocols.anchored_design.AnchoredDesignMover) -> float filter based on total complex score

get_name(...) from builtins.PyCapsule
get_name(rosetta.protocols.anchored_design.AnchoredDesignMover) -> str

get_randomize_input_sequence(...) from builtins.PyCapsule
get_randomize_input_sequence(rosetta.protocols.anchored_design.AnchoredDesignMover) -> bool randomize_input_sequence to complement loop extension in forgetting the input

get_refine_only(...) from builtins.PyCapsule
get_refine_only(rosetta.protocols.anchored_design.AnchoredDesignMover) -> bool skip the perturbation step - useful when you already have a good structure

get_rmsd(...) from builtins.PyCapsule
get_rmsd(rosetta.protocols.anchored_design.AnchoredDesignMover) -> bool run RMSD calculations

get_show_extended(...) from builtins.PyCapsule
get_show_extended(rosetta.protocols.anchored_design.AnchoredDesignMover) -> bool show_extended demonstrates that the code really forgets the input structure

get_vary_cutpoints(...) from builtins.PyCapsule
get_vary_cutpoints(rosetta.protocols.anchored_design.AnchoredDesignMover) -> bool pick a different cutpoint than the input; useful when you want to sample cutpoints

perturb_anchor(...) from builtins.PyCapsule
perturb_anchor(self : rosetta.protocols.anchored_design.AnchoredDesignMover, pose : rosetta.core.pose.Pose) -> NoneType handles perturbing the initial anchor placement

randomize_input_sequence(...) from builtins.PyCapsule
randomize_input_sequence(self : rosetta.protocols.anchored_design.AnchoredDesignMover, pose : rosetta.core.pose.Pose) -> NoneType randomize the input loop sequence.  Useful if you have reason to believe the starting loop sequence is biasing to a particular unwanted structure in centroid mode.  Acts only on designable positions.

read_options(...) from builtins.PyCapsule
read_options(rosetta.protocols.anchored_design.AnchoredDesignMover) -> NoneType read in options from the options system

reinitialize_for_each_job(...) from builtins.PyCapsule
reinitialize_for_each_job(rosetta.protocols.anchored_design.AnchoredDesignMover) -> bool

reinitialize_for_new_input(...) from builtins.PyCapsule
reinitialize_for_new_input(rosetta.protocols.anchored_design.AnchoredDesignMover) -> bool

set_RMSD_only_this(...) from builtins.PyCapsule
set_RMSD_only_this(self : rosetta.protocols.anchored_design.AnchoredDesignMover, RMSD_only_this : str) -> NoneType run only RMSD calculations against this input, don't do actual AnchoredDesign

set_autoinitialize(...) from builtins.PyCapsule
set_autoinitialize(self : rosetta.protocols.anchored_design.AnchoredDesignMover, autoinitialize : bool) -> NoneType whether to automatically initialize from the options system; defaults to true

set_delete_interface_native_sidechains(...) from builtins.PyCapsule
set_delete_interface_native_sidechains(self : rosetta.protocols.anchored_design.AnchoredDesignMover, delete_interface_native_sidechains : bool) -> NoneType delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode

set_filter_SASA(...) from builtins.PyCapsule
set_filter_SASA(self : rosetta.protocols.anchored_design.AnchoredDesignMover, filter_SASA : float) -> NoneType filter based on complex SASA

set_filter_omega(...) from builtins.PyCapsule
set_filter_omega(self : rosetta.protocols.anchored_design.AnchoredDesignMover, filter_omega : bool) -> NoneType filter based on omega angles in the loops - filter out cis omegas

set_filter_score(...) from builtins.PyCapsule
set_filter_score(self : rosetta.protocols.anchored_design.AnchoredDesignMover, filter_score : float) -> NoneType filter based on total complex score

set_fold_tree_and_cutpoints(...) from builtins.PyCapsule
set_fold_tree_and_cutpoints(self : rosetta.protocols.anchored_design.AnchoredDesignMover, pose : rosetta.core.pose.Pose) -> NoneType creates the anchored design fold tree and applies it to the pose

set_randomize_input_sequence(...) from builtins.PyCapsule
set_randomize_input_sequence(self : rosetta.protocols.anchored_design.AnchoredDesignMover, randomize_input_sequence : bool) -> NoneType randomize_input_sequence to complement loop extension in forgetting the input

set_refine_only(...) from builtins.PyCapsule
set_refine_only(self : rosetta.protocols.anchored_design.AnchoredDesignMover, refine_only : bool) -> NoneType skip the perturbation step - useful when you already have a good structure

set_rmsd(...) from builtins.PyCapsule
set_rmsd(self : rosetta.protocols.anchored_design.AnchoredDesignMover, rmsd : bool) -> NoneType run RMSD calculations

set_show_extended(...) from builtins.PyCapsule
set_show_extended(self : rosetta.protocols.anchored_design.AnchoredDesignMover, show_extended : bool) -> NoneType show_extended demonstrates that the code really forsets the input structure

set_vary_cutpoints(...) from builtins.PyCapsule
set_vary_cutpoints(self : rosetta.protocols.anchored_design.AnchoredDesignMover, vary_cutpoints : bool) -> NoneType pick a different cutpoint than the input; useful when you want to sample cutpoints

Methods inherited from rosetta.protocols.moves.Mover:

clear_info(...) from builtins.PyCapsule
clear_info(rosetta.protocols.moves.Mover) -> NoneType Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. clear_info is called by jd2 before calling apply

create(...) from builtins.PyCapsule
create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

get_additional_output(...) from builtins.PyCapsule
get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose fpd Mechanism by which a mover may return multiple output poses from a single input pose.

get_current_job(...) from builtins.PyCapsule
get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob

get_current_tag(...) from builtins.PyCapsule
get_current_tag(rosetta.protocols.moves.Mover) -> str A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag.  This functionality is not intended for use with the 2008 job distributor.

get_input_pose(...) from builtins.PyCapsule
get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_last_move_status(...) from builtins.PyCapsule
get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.

get_native_pose(...) from builtins.PyCapsule
get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_self_ptr(...) from builtins.PyCapsule
get_self_ptr(*args, **kwargs) Overloaded function. 1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover 2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

get_self_weak_ptr(...) from builtins.PyCapsule
get_self_weak_ptr(*args, **kwargs) Overloaded function. 1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t 2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t

get_type(...) from builtins.PyCapsule
get_type(rosetta.protocols.moves.Mover) -> str

info(...) from builtins.PyCapsule
info(*args, **kwargs) Overloaded function. 1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t non-const accessor 2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t const accessor

last_proposal_density_ratio(...) from builtins.PyCapsule
last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float

name(...) from builtins.PyCapsule
name() -> str

register_options(...) from builtins.PyCapsule
register_options(*args, **kwargs) Overloaded function. 1. register_options() -> NoneType Overload this static method if you access options within the mover. These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method. 2. register_options() -> NoneType 3. register_options() -> NoneType 4. register_options() -> NoneType 5. register_options() -> NoneType 6. register_options() -> NoneType 7. register_options() -> NoneType 8. register_options() -> NoneType 9. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 10. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 11. register_options() -> NoneType Associates relevant options with the SnugDock class 12. register_options() -> NoneType Associates relevant options with the SnugDockProtocol class 13. register_options() -> NoneType Register the options used by this mover with the global options system. 14. register_options() -> NoneType 15. register_options() -> NoneType Associate relevant options with the TemperedDocking class. 16. register_options() -> NoneType 17. register_options() -> NoneType 18. register_options() -> NoneType Associates relevant options with the TemperedDocking class. 19. register_options() -> NoneType 20. register_options() -> NoneType Associates relevant options with the ConstraintSetMover class 21. register_options() -> NoneType 22. register_options() -> NoneType Associates relevant options with the DockingInitialPerturbation class 23. register_options() -> NoneType Associates relevant options with the DockingProtocol class 24. register_options() -> NoneType Associates relevant options with the TemperedDocking class 25. register_options() -> NoneType 26. register_options() -> NoneType 27. register_options() -> NoneType 28. register_options() -> NoneType register options 29. register_options() -> NoneType 30. register_options() -> NoneType Registers applicable options 31. register_options() -> NoneType Register options with the option system. 32. register_options() -> NoneType 33. register_options() -> NoneType 34. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 35. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycleContainer class 36. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 37. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 38. register_options() -> NoneType 39. register_options() -> NoneType Register options with the option system. 40. register_options() -> NoneType

reset_status(...) from builtins.PyCapsule
reset_status(rosetta.protocols.moves.Mover) -> NoneType resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

set_current_job(...) from builtins.PyCapsule
set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType ////////////////////////////end Job Distributor interface////////////////////////////////////////

set_current_tag(...) from builtins.PyCapsule
set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType

set_input_pose(...) from builtins.PyCapsule
set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for poses contained for rms

set_native_pose(...) from builtins.PyCapsule
set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe

set_type(...) from builtins.PyCapsule
set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType

test_move(...) from builtins.PyCapsule
test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying

type(...) from builtins.PyCapsule
type(*args, **kwargs) Overloaded function. 1. type(rosetta.protocols.moves.Mover) -> str 2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType

class AnchoredPerturbMover(rosetta.protocols.moves.Mover)

    ////////////////////////////////////////////////////////////////////////////////////////////////////////

Method resolution order:

AnchoredPerturbMover

rosetta.protocols.moves.Mover

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(self : handle, interface_in : protocols::anchored_design::AnchorMoversData) -> NoneType 2. __init__(handle, rosetta.protocols.anchored_design.AnchoredPerturbMover) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

apply(...) from builtins.PyCapsule
apply(self : rosetta.protocols.anchored_design.AnchoredPerturbMover, pose : rosetta.core.pose.Pose) -> NoneType

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.anchored_design.AnchoredPerturbMover,  : rosetta.protocols.anchored_design.AnchoredPerturbMover) -> rosetta.protocols.anchored_design.AnchoredPerturbMover

get_debug(...) from builtins.PyCapsule
get_debug(rosetta.protocols.anchored_design.AnchoredPerturbMover) -> bool debugging mode activates a bunch of extra output

get_min_type(...) from builtins.PyCapsule
get_min_type(rosetta.protocols.anchored_design.AnchoredPerturbMover) -> str what minimizer type to use?

get_name(...) from builtins.PyCapsule
get_name(rosetta.protocols.anchored_design.AnchoredPerturbMover) -> str

get_no_frags(...) from builtins.PyCapsule
get_no_frags(rosetta.protocols.anchored_design.AnchoredPerturbMover) -> bool do not use fragments?

get_nonpivot_torsion_sampling(...) from builtins.PyCapsule
get_nonpivot_torsion_sampling(rosetta.protocols.anchored_design.AnchoredPerturbMover) -> bool use nonpivot torsion sampling for KIC?

get_perturb_CCD_off(...) from builtins.PyCapsule
get_perturb_CCD_off(rosetta.protocols.anchored_design.AnchoredPerturbMover) -> bool do not perform CCD style closure (use KIC only)

get_perturb_KIC_off(...) from builtins.PyCapsule
get_perturb_KIC_off(rosetta.protocols.anchored_design.AnchoredPerturbMover) -> bool do not perform KIC style closure (use CCD only)

get_perturb_cycles(...) from builtins.PyCapsule
get_perturb_cycles(rosetta.protocols.anchored_design.AnchoredPerturbMover) -> int number of MC cycles

get_perturb_show(...) from builtins.PyCapsule
get_perturb_show(rosetta.protocols.anchored_design.AnchoredPerturbMover) -> bool show perturb result structure?

get_perturb_temp(...) from builtins.PyCapsule
get_perturb_temp(rosetta.protocols.anchored_design.AnchoredPerturbMover) -> float MC temperature

read_options(...) from builtins.PyCapsule
read_options(rosetta.protocols.anchored_design.AnchoredPerturbMover) -> NoneType read in options from the options system

set_debug(...) from builtins.PyCapsule
set_debug(self : rosetta.protocols.anchored_design.AnchoredPerturbMover, debug : bool) -> NoneType debugging mode activates a bunch of extra output

set_min_type(...) from builtins.PyCapsule
set_min_type(self : rosetta.protocols.anchored_design.AnchoredPerturbMover, min_type : str) -> NoneType what minimizer type to use?

set_no_frags(...) from builtins.PyCapsule
set_no_frags(self : rosetta.protocols.anchored_design.AnchoredPerturbMover, no_frags : bool) -> NoneType do not use fragments?

set_nonpivot_torsion_sampling(...) from builtins.PyCapsule
set_nonpivot_torsion_sampling(self : rosetta.protocols.anchored_design.AnchoredPerturbMover, nonpivot_torsion_sampling : bool) -> NoneType use nonpivot torsion sampling for KIC?

set_perturb_CCD_off(...) from builtins.PyCapsule
set_perturb_CCD_off(self : rosetta.protocols.anchored_design.AnchoredPerturbMover, perturb_CCD_off : bool) -> NoneType do not perform CCD style closure (use KIC only)

set_perturb_KIC_off(...) from builtins.PyCapsule
set_perturb_KIC_off(self : rosetta.protocols.anchored_design.AnchoredPerturbMover, perturb_KIC_off : bool) -> NoneType do not perform KIC style closure (use CCD only)

set_perturb_cycles(...) from builtins.PyCapsule
set_perturb_cycles(self : rosetta.protocols.anchored_design.AnchoredPerturbMover, perturb_cycles : int) -> NoneType number of MC cycles

set_perturb_show(...) from builtins.PyCapsule
set_perturb_show(self : rosetta.protocols.anchored_design.AnchoredPerturbMover, perturb_show : bool) -> NoneType show perturb result structure?

set_perturb_temp(...) from builtins.PyCapsule
set_perturb_temp(self : rosetta.protocols.anchored_design.AnchoredPerturbMover, perturb_temp : float) -> NoneType MC temperature

Methods inherited from rosetta.protocols.moves.Mover:

clear_info(...) from builtins.PyCapsule
clear_info(rosetta.protocols.moves.Mover) -> NoneType Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. clear_info is called by jd2 before calling apply

clone(...) from builtins.PyCapsule
clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover Return a clone of the Mover object.

create(...) from builtins.PyCapsule
create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

fresh_instance(...) from builtins.PyCapsule
fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover Generates a new Mover object freshly created with the default ctor.

get_additional_output(...) from builtins.PyCapsule
get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose fpd Mechanism by which a mover may return multiple output poses from a single input pose.

get_current_job(...) from builtins.PyCapsule
get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob

get_current_tag(...) from builtins.PyCapsule
get_current_tag(rosetta.protocols.moves.Mover) -> str A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag.  This functionality is not intended for use with the 2008 job distributor.

get_input_pose(...) from builtins.PyCapsule
get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_last_move_status(...) from builtins.PyCapsule
get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.

get_native_pose(...) from builtins.PyCapsule
get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_self_ptr(...) from builtins.PyCapsule
get_self_ptr(*args, **kwargs) Overloaded function. 1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover 2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

get_self_weak_ptr(...) from builtins.PyCapsule
get_self_weak_ptr(*args, **kwargs) Overloaded function. 1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t 2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t

get_type(...) from builtins.PyCapsule
get_type(rosetta.protocols.moves.Mover) -> str

info(...) from builtins.PyCapsule
info(*args, **kwargs) Overloaded function. 1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t non-const accessor 2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t const accessor

last_proposal_density_ratio(...) from builtins.PyCapsule
last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float

name(...) from builtins.PyCapsule
name() -> str

register_options(...) from builtins.PyCapsule
register_options(*args, **kwargs) Overloaded function. 1. register_options() -> NoneType Overload this static method if you access options within the mover. These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method. 2. register_options() -> NoneType 3. register_options() -> NoneType 4. register_options() -> NoneType 5. register_options() -> NoneType 6. register_options() -> NoneType 7. register_options() -> NoneType 8. register_options() -> NoneType 9. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 10. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 11. register_options() -> NoneType Associates relevant options with the SnugDock class 12. register_options() -> NoneType Associates relevant options with the SnugDockProtocol class 13. register_options() -> NoneType Register the options used by this mover with the global options system. 14. register_options() -> NoneType 15. register_options() -> NoneType Associate relevant options with the TemperedDocking class. 16. register_options() -> NoneType 17. register_options() -> NoneType 18. register_options() -> NoneType Associates relevant options with the TemperedDocking class. 19. register_options() -> NoneType 20. register_options() -> NoneType Associates relevant options with the ConstraintSetMover class 21. register_options() -> NoneType 22. register_options() -> NoneType Associates relevant options with the DockingInitialPerturbation class 23. register_options() -> NoneType Associates relevant options with the DockingProtocol class 24. register_options() -> NoneType Associates relevant options with the TemperedDocking class 25. register_options() -> NoneType 26. register_options() -> NoneType 27. register_options() -> NoneType 28. register_options() -> NoneType register options 29. register_options() -> NoneType 30. register_options() -> NoneType Registers applicable options 31. register_options() -> NoneType Register options with the option system. 32. register_options() -> NoneType 33. register_options() -> NoneType 34. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 35. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycleContainer class 36. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 37. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 38. register_options() -> NoneType 39. register_options() -> NoneType Register options with the option system. 40. register_options() -> NoneType

reinitialize_for_each_job(...) from builtins.PyCapsule
reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.

reinitialize_for_new_input(...) from builtins.PyCapsule
reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

reset_status(...) from builtins.PyCapsule
reset_status(rosetta.protocols.moves.Mover) -> NoneType resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

set_current_job(...) from builtins.PyCapsule
set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType ////////////////////////////end Job Distributor interface////////////////////////////////////////

set_current_tag(...) from builtins.PyCapsule
set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType

set_input_pose(...) from builtins.PyCapsule
set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for poses contained for rms

set_native_pose(...) from builtins.PyCapsule
set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe

set_type(...) from builtins.PyCapsule
set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType

test_move(...) from builtins.PyCapsule
test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying

type(...) from builtins.PyCapsule
type(*args, **kwargs) Overloaded function. 1. type(rosetta.protocols.moves.Mover) -> str 2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType

class AnchoredRefineMover(rosetta.protocols.moves.Mover)


Method resolution order:

AnchoredRefineMover

rosetta.protocols.moves.Mover

builtins.object

Methods defined here:

__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs) Overloaded function. 1. __init__(self : handle, interface_in : protocols::anchored_design::AnchorMoversData) -> NoneType 2. __init__(handle, rosetta.protocols.anchored_design.AnchoredRefineMover) -> NoneType

__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.

apply(...) from builtins.PyCapsule
apply(self : rosetta.protocols.anchored_design.AnchoredRefineMover, pose : rosetta.core.pose.Pose) -> NoneType

assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.anchored_design.AnchoredRefineMover,  : rosetta.protocols.anchored_design.AnchoredRefineMover) -> rosetta.protocols.anchored_design.AnchoredRefineMover

get_debug(...) from builtins.PyCapsule
get_debug(rosetta.protocols.anchored_design.AnchoredRefineMover) -> bool debugging mode activates a bunch of extra output

get_min_type(...) from builtins.PyCapsule
get_min_type(rosetta.protocols.anchored_design.AnchoredRefineMover) -> str what minimizer type to use?

get_name(...) from builtins.PyCapsule
get_name(rosetta.protocols.anchored_design.AnchoredRefineMover) -> str

get_nonpivot_torsion_sampling(...) from builtins.PyCapsule
get_nonpivot_torsion_sampling(rosetta.protocols.anchored_design.AnchoredRefineMover) -> bool use nonpivot torsion sampling for KIC?

get_refine_CCD_off(...) from builtins.PyCapsule
get_refine_CCD_off(rosetta.protocols.anchored_design.AnchoredRefineMover) -> bool do not perform CCD style closure (use KIC only)

get_refine_KIC_off(...) from builtins.PyCapsule
get_refine_KIC_off(rosetta.protocols.anchored_design.AnchoredRefineMover) -> bool do not perform KIC style closure (use CCD only)

get_refine_cycles(...) from builtins.PyCapsule
get_refine_cycles(rosetta.protocols.anchored_design.AnchoredRefineMover) -> int number of MC cycles

get_refine_repack_cycles(...) from builtins.PyCapsule
get_refine_repack_cycles(rosetta.protocols.anchored_design.AnchoredRefineMover) -> int how many cycles between repack/design opportunities?

get_refine_temp(...) from builtins.PyCapsule
get_refine_temp(rosetta.protocols.anchored_design.AnchoredRefineMover) -> float MC temperature

get_vicinity_degree(...) from builtins.PyCapsule
get_vicinity_degree(rosetta.protocols.anchored_design.AnchoredRefineMover) -> float KIC vicinity sampling degrees

get_vicinity_sampling(...) from builtins.PyCapsule
get_vicinity_sampling(rosetta.protocols.anchored_design.AnchoredRefineMover) -> bool KIC use vicinity sampling?

read_options(...) from builtins.PyCapsule
read_options(rosetta.protocols.anchored_design.AnchoredRefineMover) -> NoneType read in options from the options system

set_debug(...) from builtins.PyCapsule
set_debug(self : rosetta.protocols.anchored_design.AnchoredRefineMover, debug : bool) -> NoneType debugging mode activates a bunch of extra output

set_min_type(...) from builtins.PyCapsule
set_min_type(self : rosetta.protocols.anchored_design.AnchoredRefineMover, min_type : str) -> NoneType what minimizer type to use?

set_nonpivot_torsion_sampling(...) from builtins.PyCapsule
set_nonpivot_torsion_sampling(self : rosetta.protocols.anchored_design.AnchoredRefineMover, nonpivot_torsion_sampling : bool) -> NoneType use nonpivot torsion sampling for KIC?

set_refine_CCD_off(...) from builtins.PyCapsule
set_refine_CCD_off(self : rosetta.protocols.anchored_design.AnchoredRefineMover, refine_CCD_off : bool) -> NoneType do not perform CCD style closure (use KIC only)

set_refine_KIC_off(...) from builtins.PyCapsule
set_refine_KIC_off(self : rosetta.protocols.anchored_design.AnchoredRefineMover, refine_KIC_off : bool) -> NoneType do not perform KIC style closure (use CCD only)

set_refine_cycles(...) from builtins.PyCapsule
set_refine_cycles(self : rosetta.protocols.anchored_design.AnchoredRefineMover, refine_cycles : int) -> NoneType number of MC cycles

set_refine_repack_cycles(...) from builtins.PyCapsule
set_refine_repack_cycles(self : rosetta.protocols.anchored_design.AnchoredRefineMover, refine_repack_cycles : int) -> NoneType how many cycles between repack/design opportunities?

set_refine_temp(...) from builtins.PyCapsule
set_refine_temp(self : rosetta.protocols.anchored_design.AnchoredRefineMover, refine_temp : float) -> NoneType MC temperature

set_vicinity_degree(...) from builtins.PyCapsule
set_vicinity_degree(self : rosetta.protocols.anchored_design.AnchoredRefineMover, vicinity_degree : int) -> NoneType KIC vicinity sampling degrees

set_vicinity_sampling(...) from builtins.PyCapsule
set_vicinity_sampling(self : rosetta.protocols.anchored_design.AnchoredRefineMover, vicinity_sampling : bool) -> NoneType KIC use vicinity sampling?

Methods inherited from rosetta.protocols.moves.Mover:

clear_info(...) from builtins.PyCapsule
clear_info(rosetta.protocols.moves.Mover) -> NoneType Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. clear_info is called by jd2 before calling apply

clone(...) from builtins.PyCapsule
clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover Return a clone of the Mover object.

create(...) from builtins.PyCapsule
create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

fresh_instance(...) from builtins.PyCapsule
fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover Generates a new Mover object freshly created with the default ctor.

get_additional_output(...) from builtins.PyCapsule
get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose fpd Mechanism by which a mover may return multiple output poses from a single input pose.

get_current_job(...) from builtins.PyCapsule
get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob

get_current_tag(...) from builtins.PyCapsule
get_current_tag(rosetta.protocols.moves.Mover) -> str A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag.  This functionality is not intended for use with the 2008 job distributor.

get_input_pose(...) from builtins.PyCapsule
get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_last_move_status(...) from builtins.PyCapsule
get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.

get_native_pose(...) from builtins.PyCapsule
get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose

get_self_ptr(...) from builtins.PyCapsule
get_self_ptr(*args, **kwargs) Overloaded function. 1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover 2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover

get_self_weak_ptr(...) from builtins.PyCapsule
get_self_weak_ptr(*args, **kwargs) Overloaded function. 1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t 2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t

get_type(...) from builtins.PyCapsule
get_type(rosetta.protocols.moves.Mover) -> str

info(...) from builtins.PyCapsule
info(*args, **kwargs) Overloaded function. 1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t non-const accessor 2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t const accessor

last_proposal_density_ratio(...) from builtins.PyCapsule
last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float

name(...) from builtins.PyCapsule
name() -> str

register_options(...) from builtins.PyCapsule
register_options(*args, **kwargs) Overloaded function. 1. register_options() -> NoneType Overload this static method if you access options within the mover. These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method. 2. register_options() -> NoneType 3. register_options() -> NoneType 4. register_options() -> NoneType 5. register_options() -> NoneType 6. register_options() -> NoneType 7. register_options() -> NoneType 8. register_options() -> NoneType 9. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 10. register_options() -> NoneType Associates relevant options with the AntibodyModeler class 11. register_options() -> NoneType Associates relevant options with the SnugDock class 12. register_options() -> NoneType Associates relevant options with the SnugDockProtocol class 13. register_options() -> NoneType Register the options used by this mover with the global options system. 14. register_options() -> NoneType 15. register_options() -> NoneType Associate relevant options with the TemperedDocking class. 16. register_options() -> NoneType 17. register_options() -> NoneType 18. register_options() -> NoneType Associates relevant options with the TemperedDocking class. 19. register_options() -> NoneType 20. register_options() -> NoneType Associates relevant options with the ConstraintSetMover class 21. register_options() -> NoneType 22. register_options() -> NoneType Associates relevant options with the DockingInitialPerturbation class 23. register_options() -> NoneType Associates relevant options with the DockingProtocol class 24. register_options() -> NoneType Associates relevant options with the TemperedDocking class 25. register_options() -> NoneType 26. register_options() -> NoneType 27. register_options() -> NoneType 28. register_options() -> NoneType register options 29. register_options() -> NoneType 30. register_options() -> NoneType Registers applicable options 31. register_options() -> NoneType Register options with the option system. 32. register_options() -> NoneType 33. register_options() -> NoneType 34. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 35. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycleContainer class 36. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 37. register_options() -> NoneType Associates relevant options with the LoopRefineInnerCycle class 38. register_options() -> NoneType 39. register_options() -> NoneType Register options with the option system. 40. register_options() -> NoneType

reinitialize_for_each_job(...) from builtins.PyCapsule
reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.

reinitialize_for_new_input(...) from builtins.PyCapsule
reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

reset_status(...) from builtins.PyCapsule
reset_status(rosetta.protocols.moves.Mover) -> NoneType resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

set_current_job(...) from builtins.PyCapsule
set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType ////////////////////////////end Job Distributor interface////////////////////////////////////////

set_current_tag(...) from builtins.PyCapsule
set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType

set_input_pose(...) from builtins.PyCapsule
set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for poses contained for rms

set_native_pose(...) from builtins.PyCapsule
set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe

set_type(...) from builtins.PyCapsule
set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType

test_move(...) from builtins.PyCapsule
test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying

type(...) from builtins.PyCapsule
type(*args, **kwargs) Overloaded function. 1. type(rosetta.protocols.moves.Mover) -> str 2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType